Modified AtoM Core Files

This document describes the files that differ from a pure AtoM 2.10 installation when using the AHG Framework.

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Summary

File	Type	Purpose
config/ProjectConfiguration.class.php	Replaced	Database-driven plugin loading
plugins/sfPluginAdminPlugin/.../themesAction.class.php	Patched	Theme visibility fix
plugins/qbAclPlugin/lib/QubitAcl.class.php	Patched	Role 99 duplicate fix
/etc/nginx/sites-available/atom	Modified	Framework compatibility

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1. ProjectConfiguration.class.php

Location: {ATOM_ROOT}/config/ProjectConfiguration.class.php

Type: Replaced entirely (from template)

Template: atom-framework/config/ProjectConfiguration.class.php.template

What Changed

The install script replaces AtoM's default ProjectConfiguration.class.php with a custom version that includes:

1. Framework Bootstrap Loading - Initializes Laravel Query Builder
2. Database-Driven Plugin Loading - loadPluginsFromDatabase() function

Key Addition: loadPluginsFromDatabase()

/**
 * Load plugins from atom_plugin table instead of setting_i18n
 */
protected function loadPluginsFromDatabase(array $corePlugins = []): array
{
    $plugins = $corePlugins;

    try {
        $pdo = new PDO(
            'mysql:host=' . sfConfig::get('app_database_host', 'localhost') . 
            ';dbname=' . sfConfig::get('app_database_name'),
            sfConfig::get('app_database_user'),
            sfConfig::get('app_database_password')
        );

        $stmt = $pdo->query('SELECT name FROM atom_plugin WHERE is_enabled = 1 ORDER BY load_order');
        while ($row = $stmt->fetch(PDO::FETCH_ASSOC)) {
            if (!in_array($row['name'], $plugins)) {
                $plugins[] = $row['name'];
            }
        }
    } catch (PDOException $e) {
        // Fallback to core plugins only
    }

    return $plugins;
}

Why This Change

• Before: AtoM loads plugins from setting_i18n table (id=1), a serialized PHP array
• After: Plugins loaded from atom_plugin table with proper fields (is_enabled, load_order, is_locked)
• Benefit: Enables CLI management, plugin auditing, and prevents accidental disabling of critical plugins

Legacy Compatibility

The setting_i18n table (id=1) is still maintained for: - The sfPluginAdminPlugin UI (Admin → Plugins) - Backwards compatibility with AtoM core code

When a plugin is enabled via CLI, both tables are updated.

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2. themesAction.class.php

Location: {ATOM_ROOT}/plugins/sfPluginAdminPlugin/modules/sfPluginAdminPlugin/actions/themesAction.class.php

Type: Patched (specific lines modified)

What Changed

Removed the loop that filters out enabled plugins from the theme list.

Original Code (lines 43-46)

foreach (sfPluginAdminPluginConfiguration::$pluginNames as $name) {
    unset($pluginPaths[$name]);
}

Patched Code

// Removed: themes should remain visible even when enabled
// foreach (sfPluginAdminPluginConfiguration::$pluginNames as $name) {
//     unset($pluginPaths[$name]);
// }

Why This Change

Problem: AtoM's default behavior removes enabled plugins from the themes list. When ahgThemeB5Plugin is enabled, it disappears from Admin → Themes, making it impossible to switch or view theme settings.

Root Cause: Symlinks from plugins/ to atom-ahg-plugins/ resolve to their real path, which doesn't match sf_plugins_dir, causing theme detection to fail for enabled plugins.

Solution: Don't filter out enabled plugins - themes should always be visible in the list.

Additional Fixes in This File

1. Unserialize Fallback (line ~80):

   // Before
   $settings = unserialize($setting->getValue(['sourceCulture' => true]));
   
   // After
   $settings = unserialize($setting->getValue(['sourceCulture' => true])) ?: [];
   

2. Try/Catch around Plugin Instantiation - Prevents fatal errors if a plugin class fails to load

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3. QubitAcl.class.php

Location: {ATOM_ROOT}/plugins/qbAclPlugin/lib/QubitAcl.class.php

Type: Patched (specific method modified)

What Changed

Added in_array checks in buildUserRoleList() method to prevent duplicate role registration.

Original Code

protected function buildUserRoleList($user)
{
    // Don't add user twice
    if (in_array($user->getUserID(), $this->_roles)) {
        return $this;
    }

    $parents = [];

    if ($user->isAuthenticated()) {
        // Add authenticated group
        $this->acl->addRole(QubitAclGroup::getById(QubitAclGroup::AUTHENTICATED_ID));
        $this->_roles[] = QubitAclGroup::AUTHENTICATED_ID;

        // Add groups (if user belongs to any)
        if (0 < count($aclUserGroups = $user->user->getAclUserGroups())) {
            foreach ($aclUserGroups as $aclUserGroup) {
                $aclGroup = $aclUserGroup->group;
                $this->acl->addRole($aclGroup, $aclGroup->parent);
                $this->_roles[] = $aclGroup->id;
                $parents[] = $aclGroup->id;
            }
        }
        // ...
    }
}

Patched Code

protected function buildUserRoleList($user)
{
    // Don't add user twice
    if (in_array($user->getUserID(), $this->_roles)) {
        return $this;
    }

    $parents = [];

    if ($user->isAuthenticated()) {
        // Add authenticated group (check first to avoid duplicate)
        if (!in_array(QubitAclGroup::AUTHENTICATED_ID, $this->_roles)) {
            $this->acl->addRole(QubitAclGroup::getById(QubitAclGroup::AUTHENTICATED_ID));
            $this->_roles[] = QubitAclGroup::AUTHENTICATED_ID;
        }

        // Add groups (if user belongs to any)
        if (0 < count($aclUserGroups = $user->user->getAclUserGroups())) {
            foreach ($aclUserGroups as $aclUserGroup) {
                $aclGroup = $aclUserGroup->group;
                if (!in_array($aclGroup->id, $this->_roles)) {
                    $this->acl->addRole($aclGroup, $aclGroup->parent);
                    $this->_roles[] = $aclGroup->id;
                }
                $parents[] = $aclGroup->id;
            }
        }
        // ...
    }
}

Why This Change

Problem: When a user is in acl_user_group with group_id = 99 (Authenticated), the code: 1. First adds role 99 (AUTHENTICATED_ID) for all authenticated users 2. Then loops through user's groups and tries to add 99 again 3. Zend ACL throws: Role id '99' already exists in the registry

Error Message:

500 | Internal Server Error | Zend_Acl_Role_Registry_Exception
Role id '99' already exists in the registry

Solution: Check in_array before calling addRole to prevent duplicates.

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4. Nginx Configuration

Location: /etc/nginx/sites-available/atom (or similar)

Type: Modified for framework compatibility

Standard AtoM Configuration

location ~ ^/(index|qubit_dev)\.php(/|$) {
    include /etc/nginx/fastcgi_params;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
    fastcgi_split_path_info ^(.+\.php)(/.*)$;
    fastcgi_pass unix:/run/php/php8.3-fpm.sock;
}

AHG Framework Configuration

No changes required to nginx for basic framework operation. The framework integrates through PHP, not nginx.

Optional: PHP-FPM Pool Configuration

If using auto_prepend_file (alternative loading method):

Location: /etc/php/8.3/fpm/pool.d/atom.conf

; AtoM Framework - auto-prepend (optional, not currently used)
; php_admin_value[auto_prepend_file] = /usr/share/nginx/atom/atom-framework/prepend.php

Current Method: Framework is loaded via ProjectConfiguration.class.php bootstrap, not auto_prepend.

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Applying Patches

During Fresh Install

The bin/install script automatically applies all patches:

cd /usr/share/nginx/atom/atom-framework
bash bin/install

Manual Patch Application

If patches need to be reapplied (e.g., after AtoM upgrade):

# 1. ProjectConfiguration - just re-run install
cd /usr/share/nginx/atom/atom-framework
bash bin/install

# 2. themesAction.class.php - comment out the unset loop
# Find lines with: foreach (sfPluginAdminPluginConfiguration::$pluginNames
# Comment out the foreach block

# 3. QubitAcl.class.php - add in_array checks
# The install script includes a PHP patcher for this

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After AtoM Upgrades

When upgrading AtoM core:

1. ProjectConfiguration.class.php - Will be overwritten. Re-run bash bin/install
2. themesAction.class.php - May be overwritten. Check and re-patch if needed
3. QubitAcl.class.php - May be overwritten. Re-run install (includes auto-patch)

Verification Commands

# Check ProjectConfiguration has loadPluginsFromDatabase
grep -c "loadPluginsFromDatabase" /usr/share/nginx/atom/config/ProjectConfiguration.class.php

# Check themesAction has the fix (should show commented lines)
grep -c "Removed: themes should remain" /usr/share/nginx/atom/plugins/sfPluginAdminPlugin/modules/sfPluginAdminPlugin/actions/themesAction.class.php

# Check QubitAcl has the fix
grep -c "check first to avoid duplicate" /usr/share/nginx/atom/plugins/qbAclPlugin/lib/QubitAcl.class.php

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File Checksums

For verification after upgrades:

# Generate checksums of patched files
md5sum /usr/share/nginx/atom/config/ProjectConfiguration.class.php
md5sum /usr/share/nginx/atom/plugins/sfPluginAdminPlugin/modules/sfPluginAdminPlugin/actions/themesAction.class.php
md5sum /usr/share/nginx/atom/plugins/qbAclPlugin/lib/QubitAcl.class.php

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Troubleshooting

Plugins Not Loading

1. Check ProjectConfiguration.class.php has loadPluginsFromDatabase()
2. Verify atom_plugin table exists and has enabled plugins
3. Clear cache: php symfony cc

Theme Not Visible in Admin

1. Check themesAction.class.php patch is applied
2. Verify symlink exists: ls -la plugins/ahgThemeB5Plugin
3. Clear cache and restart PHP-FPM

Role 99 Error on Login

1. Check QubitAcl.class.php patch is applied
2. Verify with: grep "check first to avoid duplicate" plugins/qbAclPlugin/lib/QubitAcl.class.php
3. Re-run install script if patch is missing